The Smart Amplification process, version 2 (SMAP-2), also known as SmartAmp-2, is a rapid polymorphism detection system based on a unique asymmetric primer design, including a folding primer (FP) and a turn-back primer (TP) [1]. Combined with Thermus aquaticus MutS (Taq MutS) protein in an isothermal amplification procedure, the technique enables suppression of mis-amplification of highly related sequences (e.g., a wild-type sequence versus an SNP variant), minimizing background amplification. The Taq MutS protein binds to mis-matched nucleotides in erroneously primed dsDNA and prevents further amplification by blocking the dissociation of DNA duplexes having a mis-match by DNA polymerases having strand displacement activity. SmartAmp-2 assays have been used for detection of various SNPs and mutations, e.g., in ALDH2 and EGFR genes [1,2]. In the study presented here, we investigated whether this assay principle could be adapted for detection of microsatellite polymorphisms showing copy number differences in more